Background Very few studies have investigated psychopathology in children of mothers with eating disorders (ED). We aimed to determine the effect of maternal ED on childhood psychopathology in a large population‐based cohort and investigate relevant risk pathways using structural equation modeling (SEM). Methods Data on emotional and behavioral problems at 3½ years were obtained prospectively on 8,622 children from the Avon Longitudinal Study of Parents and Children (ALSPAC). Children of exposed women who self‐reported lifetime anorexia nervosa (AN, N = 193) or bulimia nervosa (BN, N = 158) in pregnancy were compared with children of unexposed women (N = 8,271) using linear and logistic regression models. SEM was used to determine best‐fitting risk models by child gender. Results There was evidence that girls of AN women were more likely to have emotional, conduct, and hyperactivity disorders [Odds Ratio (OR): 1.7 (95% Confidence Intervals 1.0–3.0); OR: 2.2 (1.2–4.0); OR: 1.8 (1.1–3.1), respectively] and boys of AN women to have emotional disorders compared with unexposed [OR: 2.0(1.2–3.4)]. Girls of women with BN were more likely to show hyperactivity [OR: 1.7 (1.0–3.1)]; and boys to show emotional and conduct disorders compared with unexposed [OR: 2.2 (1.2–3.9); OR: 2.4 (1.4–4.2), respectively]. SEM models showed that pregnancy anxiety and depression mediated the effect of maternal ED on child psychopathology. Conclusions Maternal ED are associated with different childhood psychopathology outcomes in boys and girls. Pregnancy anxiety and depression and active ED symptoms are important mediators of risk and are preventable; the direct effect of maternal lifetime ED was small.